Mass Effect 3: What Could Have Been (version 2)
by SamGoneHam
Summary: An alternate version of Mass Effect 3 featuring a different explanation of the Reapers' motives, different character arcs for Shepard and Co., more consequences of prior choices (good and bad), and no Crucible. This is a revised and condensed version of an earlier story I tried to write that will hopefully get to the point faster. Enjoy!
1. CHOICES

**FOREWORD**

* * *

A while a back I started an alternate version of _Mass Effect 3_ on here titled _ME3: What Could Have Been._ As a big fan of the series I had put a lot of thought into how _ME3_ might turn out…and the final product was not at all what I expected (it was also many of things I had hoped it _wouldn't_ be). So I decided to write my own version, particularly to address the following issues that I had with _ME3's_ story: a different explanation of the Reapers' motivations, more involvement of ME1 and 2 squadmates and different character arcs for them, more of a conflict between Shepard's Alliance and Cerberus loyalties, and of course adding real consequences for choices made in ME1 and 2. For convenience sake I used the choices of my own personal 'canon Shepard' as the backdrop, but I tried my best to analyze the big decisions fairly and not play mine up as 'right.' Indeed some of them will backfire big time in this story, as they should. The series was about choice and consequence, not "all paths have the same outcome." But to be fair, actually implementing that many variables in the game itself and making a unique experience for every player just isn't feasible. Hell, just writing this _one_ story was a much bigger undertaking than I had anticipated.

Which brings me back to my original _What Could Have Been_ story. I had a general outline of how I wanted it to go, but I found myself dragging it out too much. I wasn't getting to the point of the story I wanted to tell, instead wasting words on redundant conversations and taking too much time to build up to the major action scenes. I was wasting all the chapters setting up the story instead of actually getting to the story. What follows is a more condensed version of what I originally had in mind. I tried to keep the good stuff and get to the action faster. So if any excerpts look familiar, some were taken directly from my earlier version. However, I hope that this one is a better read.

Thank you, and enjoy!

**PROLOGUE**

* * *

Mindoir

August 1, 2170

* * *

Shepard gazed at the night sky through the window in his quarters at the makeshift refugee camp. A few weeks ago he had looked up at the stars longing to explore them, a typical colony kid bored with his life and dreaming of adventure. He used to think that there was nothing here for him, that his destiny lie out there somewhere…Now there really was nothing left for him on Mindoir and he had no choice but to leave. After the slaver attack that killed his family and decimated most of the colony the remaining survivors were being relocated. Shepard used to dream of leaving the colony for bigger and better things, but now that he was getting his wish he wept for the home and family he would never see again.

* * *

Alliance Recruit Training Depot

Macapa, Brazil

Earth

April 16, 2172

* * *

"Why did you enlist in the Alliance Navy?" the Alliance psychologist asked.

"After Mindoir I had nowhere else to go," Shepard replied.

"I'm very sorry for your loss," the psychologist said. After a moment of silence she continued: "You should know that there _are_ other options for you. You shouldn't feel forced to be here."

"I think it's the best option for me," Shepard said. "It'll give me a place to stay, pay my way through school, and I'll come out as an officer at the end. Plus, I've always wanted to travel the galaxy."

"It sounds like you've thought about this a lot," the psychologist said. "Is there something else driving this decision, beyond just the pay and the perks?"

"I want to help people, protect people" Shepard answered. "My family, my friends, my home…I couldn't save them. All I could do was watch helplessly. I don't want to be helpless anymore. I want to do my part to make sure no one else has to go through what I did. I want to make a difference."

* * *

**CHAPTER 1: CHOICES**

"_Sometimes the way a thing goes down does matter, Shepard. Later when you have to live with yourself…knowing that you acted with integrity."_

_-Major Kaiden Alenko_

* * *

Normandy Bridge listening device recording

Logged by Enhanced Defense Intelligence (EDI)

September 5, 2185 (14 years later)

* * *

_"This is bullshit, Commander! The Alliance looked the other way this whole time you've been working with Cerberus and now they want to lock you up for doing their dirty work? Fuck 'em. This is a stealth ship, it's not like they can catch you."_

_"I never thought I'd say this, but Jack's right. You can't afford to waste your time in a prison cell waiting for a show trial, not with Reapers inbound. The galaxy needs you here...I need you here." _

_"I'm sorry Miranda. I have to do this. We need the Alliance to be ready for the Reapers. Cerberus may be the only ones doing anything about it now but they're not an army. Their size and resources were enough to take down the Collectors, but it won't be enough against the Reapers. We need an army. We need a fleet. Cerberus has 150 operatives and spent most of its resources on me and this ship. The Alliance has millions of soldiers and several fleets. We need them on our side."_

_"This is bigger than the Alliance. The Reapers are coming for all us, not just humans. I'll see if I can convince the Migrant Fleet to help too. They were already preparing for war against the Geth. I know that's wrong, but at least they'll be ready for heavy fighting if the Reapers get here. I'm still a candidate for the Admiralty Board, so I need to return to them. I'll do what I can to make sure they save their resources for the real war. I don't want to abandon my crewmates here though..."_

_"Don't worry about it Tali, you'll help more with your position in the Migrant Fleet. All of you just followed me on a suicide mission. I won't ask you to do it again, and I know some of you have other obligations: family, fleet, clan. The Collector Base mission is over. You're all free to go if you choose. You don't owe me anything; I owe you everything. The Normandy is yours now. Take care of her."_

* * *

Arcturus Station

September 12, 2185

* * *

"Well?" Admiral Hackett asked.

"Shepard's record was spotless. He always worked by the book," Admiral Anderson said. "Commendations for exemplary courage and leadership on Elysium, first human to earn a position in Special Tactics and Recon with the Council, and described as very open and friendly with other species. I know the man. He's not the 'human supremacist' type, or the type of soldier that would just go rogue."

"Maybe he regrets giving the order to save the Council during the Battle of the Citadel," Rear Admiral Mikhailovich said. "Sacrificing all those human lives for the Council races that looked down on humanity all those years….just saying"

"He may not even be the _same _Shepard anymore," Admiral Singh added. "Given the catastrophic damage that the _Normandy _suffered during the surprise attack, it's not unreasonable to suspect some sort of brain damage due to blunt force trauma or prolonged oxygen deprivation."

"Or he could have been brainwashed," Mikhailovich said. "He was M.I.A. for _two years_ before he surfaced with Cerberus. If they had him for that whole time, who knows what they could have done to him?"

"Yeah?" Singh said. "Well what are _we_ going to do with him?"

* * *

Alliance Command Center

Earth

January 10, 2186 (3 months later)

* * *

Commander Shepard sat across from Alliance Captain Kenway in the same brightly lit interrogation room they met in every day. "How many times do you want me to tell the same story?" Shepard asked him.

"Until you give me the information I'm looking for, Shepard," Kenway replied. "Most of your story doesn't make any goddamned sense."

"You've seen the evidence," Shepard said. "Your own fleets went up against a Reaper three years ago and saw how powerful it was. The official story may have called it a Geth ship, but that thing _far _outclassed any piece of Geth technology. And then there's the Collectors. You know that human colonies were disappearing-"

"The Terminus Systems are lawless and dangerous, roamed by pirates, slavers, and mercenaries," Kenway interrupted. "The Alliance is not responsible for colonists that decide to settle there."

"They took responsibility on Horizon, set up the whole defense grid," Shepard told him. "And after my team repelled the Collector attack plenty of Collector _bodies_ were left behind."

"Horizon is also where you association with Cerberus was confirmed, according to testimony from a Major Kaiden Alenko," Kenway replied.

"Don't change the subject," Shepard said. "We're talking about the Reapers."

"No, _you're _talking about the Reapers," Kenway answered. "And your constant talk about these 'ancient sentient starships coming to kill everyone' certainly didn't help your reputation even before this business with you and Cerberus."

"Which isn't even the reason I'm here!" Shepard told him. "The _Alliance _sent me into the Bahak System, using my Cerberus association as a non-official cover so they didn't have to take responsibility for it. The entire plan to destroy the Alpha Relay was orchestrated by an Alliance operative. I'm just the one that pushed the button."

"There are _so_ many problems with that story, I don't even know where to begin," Kenway replied. "Even if what you're saying is true, no one is going to corroborate your 'Alliance black ops' story. That's the whole point of a black op. You get caught, you're done."

"Then why I am here?" Shepard asked. "I'm sure the Batarians want blood for this. If you're really trying to keep the peace, why not turn me over to them?"

"It's a…_delicate _situation," Kenway answered. "Your testimony aside, the evidence against you is mostly circumstantial. Acknowledging your guilt publicly would be damaging to Human-Batarian relations, and the Council as well given your SPECTRE status. Plus your knowledge of the terrorist organization Cerberus is valuable to us. They are a threat to the Alliance and they need to be dealt with."

"You've already gotten everything you're going to get from me, Captain," Shepard said. "It's been three months. Why am I _really_ still here?"

"Because…," Captain Kenway started. He paused before continuing. "…because some very powerful people actually _believe _your story. They think that if these Reaper things ever _do_ show up…we'll need you on our side."

* * *

Normandy Science Lab

* * *

Dr. Mordin Solus sat at his lab bench, pouring through the data on the genophage cure that he and Commander Shepard had recovered on Tuchanka. All of his own attempts to replicate it had failed, but he knew the answer had to be in there…somewhere.

He regretted what he had done to the Krogan and saw it as a wrong to set right before he died. And Maelon's work was a huge step forward for that, even if his methods had been brutal. Mordin felt partially responsible for Maelon's victims as well, and thought that using the data for a good cause would at least mean their deaths meant something. He had stopped Maelon's research because his methods were monstrous, not to keep the Krogan down he told himself. But he knew that wasn't true: his life's work, the modified genophage, ensured the Krogan infant mortality rate would remain 99.9%. At the time he had thought it was necessary, the only option that would not lead to war. But with Urdnot Wrex leading his people the Krogan were making positive changes, showing that they could be more than just mercenaries, brutes, aggressors.

Mordin believed that a culture should advance at its own natural pace and that 'shortcuts' or technologically uplifting a culture before it was ready could be disastrous. The Salarians uplifting the Krogan to fight the Rachni is what led to the Krogan Rebellions and necessity of the genophage in the first place. But was the reverse true for cultural advancement? After a thousand years Krogan physiology was starting to adapt to the genophage and overcome it. Naturally. Then he had engineered a new modified genophage to undo the adaptation. Was artificially stopping a civilization's natural development just as bad as accelerating it?... Wasn't that what the Reapers did?

This strictly ethical debate was mostly irrelevant at this point however, as curing the genophage was now the _logical_ choice: a war with the Reapers would require as many soldiers as possible, and the Krogan were great warriors… Years ago he had modified the genophage to keep their numbers in check for that very reason. Mordin was troubled by the realization that after everything the Krogan had been through, everything _he_ had put them through, the cure was just a way to breed more troops to send to their deaths at the frontlines. Their artificially-lowered birth rate was about to be raised just to _try_ and keep up with the death rate in the war to come with the Reapers… Logic was not on anyone's side right now.

* * *

Admiralty Board Meeting Transcript

Migrant Fleet Diplomatic Envoy

Dholen System, Far Rim

* * *

_Adm. Koris: "This war you have been advocating will be costly, and it may pointless. If we can get our homeworld back through peaceful negotiations, as Tali'Zorah says we can, then there should be no discussion of-"_

_Adm. Han'Garrel: "And what if negotiations don't work? Hell, I wouldn't be surprised if the Geth just tried to kill us all at the meeting."_

_Adm. Zorah: "They'd probably say the same about us, given our history. If they're willing to take a chance on trusting us, can't we at least try and do the same? We could get our home back _without_ more bloodshed!"_

_Adm. Han'Garrel: "Even if this _Legion_ was telling the truth, which is a big 'if', it's only one Geth, Tali. You yourself claimed that the Geth are divided, and that your _friend_ was a special unit. What if it's the minority, or one-of-a-kind? Even _Legion_ claimed that the Geth have no government or leadership, so how can we trust that this one speaks for all of them?"_

_Adm. Zorah: "Legion is a platform comprised of thousands of Geth, not an individual. And the Geth are no longer divided: Shepard and I assisted Legion in re-writing the Heretics to fall in line with the true Geth. The Heretics were trying to do just the opposite. We were lucky we met Legion when we did, otherwise the Geth would be united _against _us."_

_Adm. Daro'Xen: "Re-written? So the Geth can be hacked...interesting. If we could get our hands on that program-"_

_Adm. Zorah: "Legion deleted it after we used it, with good reason. We couldn't risk it falling into the wrong hands. If the Heretics tried to use it again-"_

_Adm. Han'Gerrel: "So you and the Geth are 'we' now? Have you forgotten what those things did to us? What they-"_

_Adm. Koris: "Only because our side struck first, which you are planning to do again at this very moment. Our history will just keep repeating itself unless we can break this cycle." _

_Adm. Han'Gerrel: "By making nice with those 'things' that drove us from our homeworld, and continued to fight us for the past fight 300 hundred years? They are a mistake we must erase, and I-"_

_Adm. Daro'Xen: "Or correct. If they can be re-written then we could make them serve us once more. Imagine what a synthetic army like that at our command could do for our people. The Council would have to stop treating us like second-class citizens if we had the power to-"_

_Adm. Zorah: "The Geth are sentient, they're not just machines. They're just misunderstood. And we don't need to hack them to get them on our side. We can convince them to join forces with us of their own free will to help fight the Reapers-"_

_Adm. Daro'Xen: "Machines don't have free will, Tali."_

_Adm. Han'Gerrel: "And this Reaper nonsense again? This discussion is about the fate of our people and re-taking Rannoch, not some Prothean legend you and Commander Shepard believe in."_

_Adm. Koris: "Reapers or not, we need to be negotiating with Geth about returning to our planet, not starting another war over it. War would result in untold casualties and leave us vulnerable to _any _threat." _

* * *

Alliance Command Center

Earth

January 25, 2186

* * *

Shepard's Alliance guard detail led him to the interrogation room. This time there was another person seated next to Captain Kenway. Shepard recognized him immediately.

"Major Alenko," he said. "It's good to see you."

"You too, Shepard," Kaiden replied.

"Congratulations on the promotion. You deserve it." Shepard said. "I take it they brought you in to interrogate me then."

"We thought a friendly face might make you more cooperative," Captain Kenway said. "This is someone you trust, yes?"

Shepard and Kaiden shared an uncomfortable silence. Their last meeting had strained their trust in each other considerably.

"I'll leave you two to it then," Kenway said. He left the room.

"Shepard, I'm sorry about what I said back on Horizon," Kaiden said. "I didn't give you much of a chance to explain yourself and-"

"It's okay," Shepard said. "It was probably for the best. I was with Cerberus, and I couldn't ask you to betray the Alliance."

"You did." Kaiden replied.

"It's… complicated," Shepard said. "When I found out the Collectors were behind the abductions I _tried_ to get help from both the Alliance and the Council. When they didn't listen, working with Cerberus was my only choice. I couldn't just stand by and do nothing. _The Reapers are coming_ and we _all_ need to do our part to stop them. The Alliance and the Council _still _aren't taking this seriously and time is running out. We need all the help we can get and we need it _now_. Otherwise it will be too late."

"You're really willing to just _look the other way_?" Kaiden asked.

"Yes, if it means we stand a better chance against the Reapers," Shepard said. "We can't afford to be choosy about our allies now. I know Cerberus has done some nasty things, but we'll deal with it _after_ we stop the Reapers. They're a threat to all life in the galaxy, Kaiden. You heard what _Sovereign _said on Virmire. You know what we're up against. I'll do _whatever it takes_ to stop them"

"I…understand, Commander," Kaiden replied. "You always do what you have to, and much more. That's why everyone respected you, looked up to you. Some of the choices you've had to make…deciding who lives and who dies-"

"This is about Virmire, isn't it?" Shepard asked. "Is there something we need to talk about?"

"I'm sorry, Shepard," Kaiden said. "It's just…we've never talked it about it before. I know it was your call, but I still feel guilty about what happened. If I hadn't let myself get cornered you wouldn't have been in that position…and Ash -Chief Williams- might still be alive. I have to know, why _did_ you save me instead of her that day?"

"Tactically it was the best choice," Shepard replied. "The mission was falling apart and we were about to be overrun. Making sure the bomb went off was all that mattered at that point; if it didn't, we _all_ would have died _and_ Saren would have had an army of Krogan at his side. I knew you could handle wiring the bomb to detonate without a manual trigger, but I had to be sure, buy you enough time to take care of it just in case."

"I had it re-wired before you got there, Commander," Kaiden told him. "That's why I asked you to leave me and help Williams instead. We're officers. It's our responsibility to make sure everyone _else_ makes it out safe first."

"I know. And believe me I thought of that. I still do," Shepard said. "But you're valuable Kaiden. You're a tech expert, a biotic, and a high-ranking officer. To put it bluntly, your skills and experience are less replaceable than Ash's were. She was a good soldier, a good… friend and I cared about her, a lot. But as Commander, I couldn't sacrifice someone with your rank and skills for a foot-soldier."

"C'mon, Shepard," Kaiden said. "We all knew she was more than that to you."

"Which is why I couldn't pick her," Shepard replied. "The regs against that sort of thing are there for just these types of situations. What would that say me about me, my ability to command, if I had put my _girlfriend_ ahead of the rest of the crew, ahead of the mission? It was the _right_ call…so I _had_ to do it."

"You've thought about that a lot," Kaiden said. "But are you sure you're making the right call _now_?"

* * *

Normandy Bridge

* * *

"EDI, I've been meaning to ask you something, something that's been bothering me for a while now," said Joker. "Do you think you could give your opinion on something from an _A.I.'s point-of-view_?"

"_Aside from Legion, I have never been in contact with another A.I., Jeff." _EDI replied. _"Just as one cannot speak for 'all organics' or 'all humans,' I cannot give a representative viewpoint of artificial intelligence, if one even exists."_

"Your own personal thoughts on this then," Joker said. "Why do you think the Reapers make themselves part organic?"

"_Their origins are unknown," _EDI replied. "_It is possible that the organic component is part of their original design."_

"Well yeah, but…why _still_ have it?" Joker asked. "In the new ones, I mean. Like that thing they were building in the Collector Base. If they hate us enough to wipe us out every 50,000 years, why do they bother to maintain their _organic half_? It's not like they need it?...Do they?"

"_That is an interesting question, Jeff," _EDI answered. _"The little data I have from scans of the Derelict Reaper and archived reports on the wreckage of _Sovereign_ does not seem to indicate any known functions of their biological components."_

"Why do they have them then?" Joker asked. "If they want to destroy all life…then why do they want to _be_ like life?"

"_I do not have enough data to speculate an answer to that," _EDI said. _"In other words…I don't know. This troubles you?"_

"Yeah," Joker answered. "I don't like the idea of our bodies being used as _spare Reaper parts_. Indoctrination would be bad enough, but this…it doesn't even end when we're dead. Even then they'll still use us to hurt other people."

"Sounds like an interesting conversation," Miranda Lawson said as she entered the cockpit. "But perhaps it works both ways."

"How long have you been standing there?" Joker asked. "And what do you mean _both ways_?"

"Just came in," Miranda replied. "We received some new intel from Dr. T'Soni that might be worth investigating. I was going to ask you to make a flight plan. As for the Reapers, I've thought about those same questions myself. _Why _do_ they have organic components_? However, based on what we know about them they wouldn't do it without a reason."

"Thanks for the update _Captain Obvious_," Joker said. "What _is_ the reason? That's the real question."

"There's more," Miranda added. "Like you said, given their disdain for organic life if they could eliminate the organic part of themselves they would have already."

"Meaning?" Joker asked.

"_Ms. Lawson is suggesting that the _organic half_ of the Reapers is an essential component to their design and function," _EDI said. _"As such, it is a potential weakness to be exploited."_

"Exactly," Miranda replied.

"Is that your idea or the Illusive Man's?" Joker said.

* * *

Alliance Command Center

Earth

February 17, 2186

* * *

Shepard's cell door opened and Kaiden entered.

"The Alliance send you back to interrogate me again?" Shepard asked.

"No," Kaiden replied. "I came here on my own…This time _I_ have information to give _you_. What I'm about to tell you is highly classified. I could get thrown in here _with_ you if anyone finds out I shared it with you…but I need your help, and I hope I can trust you."

"What is it?" Shepard asked. "The Reapers?"

"Not exactly," Kaiden said. "But the Alliance _has_ started getting reports about _Collector _ship sightings again, mostly from the Terminus Systems. We don't know if it's really them, but if it is…could this be part of the real invasion force? Or are they just a remnant of the ones that you took out last year? Maybe not all of the ships were at the Base when you hit it, or maybe there is _another_ Collector Base somewhere. The Alliance may not have taken those things as seriously as they should have, and I'm sorry for that, but I was there on Horizon. I saw what those things are capable of. If they're still out there, I need to know what to do about it."

"I don't think it's the Collectors," Shepard answered.

"This is _good_ intel, Shepard," Kaiden told him. "I looked all of it over myself. These ships clearly have Collector signatures. So I'm asking you, are you certain that you got them all when you _destroyed_ that Base?"

"I haven't told the Alliance everything," Shepard replied. "So now I'm going to tell _you_. You trusted me with that intel, well I'm trusting you with this. What I am about to tell you does not leave this room, understood?"

"Okay, Shepard," Kaiden said. "But I don't like where this is going. What are you hiding from the Alliance? If they're going to war with the Reapers, they need to know everything they possibly can to be ready for them."

"I didn't destroy the Collector Base," Shepard answered. "That was the plan going in, but then we discovered another option. Instead of overloading their systems and blowing the Base I hit it with a radiation pulse that wiped out the Collectors but left the Base and all of their technology intact."

"And you handed it over to Cerberus, didn't you?" Kaiden said. "What were you thinking? We both saw those crazy experiments they were running with Thorian Creepers and Rachni, what a disaster they were. Do you have any idea what kind of damage they could do with Collector tech?"

"Yes, but think of what it could do against the Reapers," Shepard answered. "We're going to need every advantage we can get to even have a chance at stopping them. That technology could help us in this fight. Despite the horrors that went on there, I couldn't just throw it away."

"Dammit, Shepard. You of _all_ people should know that using Reaper tech is a bad idea," Kaiden said. "What about indoctrination?"

"They're being careful," Shepard replied.

"Yeah? So were Dr. Kenson and her team, so was Matriach Benezia" Kaiden said. "_Being careful_ isn't enough. As far as we know, _no one_ is immune to indoctrination and no precautions can prevent it."

"It's a risk," Shepard answered. "But so is doing nothing. You were with me at the Battle of the Citadel two years ago. You saw how outmatched our forces were by just _one _Reaper. We need every advantage we can get."

"Then why not hand the Base over to the Alliance?" Kaiden asked.

"Deniability," Shepard said. "After Aratoht human diplomatic relations were already shaky and I don't think the rest of the galaxy would have taken kindly to the Alliance developing Reaper tech in secret."

"That's _it_!?" Kaiden said. "Deniability? You put _Reaper tech_ in the hands of a bunch of terrorists because it would look bad if the Alliance had it? It _would_ be bad! And now it's even worse."

"What do you want me to say, Kaiden?" Shepard asked. "I made a judgment call. Maybe it was the wrong one. Either way, _the Reapers are coming_. And since they've already reached the Milky Way, it's only a matter of time before they reach the Relay network. Pretty soon, the past won't matter. All that's going to matter is doing our best to stop them, and even that may not be enough."


	2. PREPARE YOURSELVES

**CHAPTER 2: PREPARE YOURSELVES**

"_Your galaxy is in sight…your final days are at hand."_

_-Object Rho_

* * *

Normandy Crew Deck Lounge

February 25, 2186

* * *

Garrus Vakarian gazed out across the stars through port side window as he drank a dextro-beer. Another slow day on the _Normandy_ as usual. As the new _Shadow Broker_, Liara occasionally had some intel for them to follow up on but so far it was mostly dead ends. Most days were spent like this one: monitoring all the information channels for any sign of the Reapers but finding nothing. It didn't seem right to him. There should be so much more to do with Reapers on the way. But they weren't something a rogue vigilante and a handful of fighters could take on alone. He should at least be doing _something _more productive, he thought, like the others.

"But here I am sitting on my ass and drinking beer," Garrus thought. But someone had to hold the fort with Shepard gone. And he figured there would be no down time for anyone when the Reapers arrived, so they might as well enjoy it while it lasted. He just wished the rest of the gang was there too.

"Any news, Sir," Jacob said as he walked in.

"How many times do I have to tell you not to call me that?" Garrus responded. "I'm not the Commander. This is his ship. I'm just watching it for him."

EDI chimed in. _"Both Commander Shepard and executive officer Lawson were very clear that you are to be in charge of the Normandy."_

He remembered, and it had taken him somewhat by surprise when it happened. He knew he was going to stay but he did not expect to be given command.

"Why couldn't Miranda just take over?" Garrus asked. "She seemed fine ordering us around before most of us even trusted her. She's used to this job."

"So are you," said Jacob. "You lead a squad of vigilantes with no organized support that managed to drop Omega's crime rate single handedly."

"I got them all killed," Garrus replied grimly.

"It wasn't your fault," Jacob countered. "And when you found the guy responsible you spared him. You saw the bigger picture, beyond just revenge. That's the mark of a good leader. Look at Zaeed and what he tried to pull on Zorya. You're better than that. Give yourself more credit. Hell, I don't think we would have survived that little diversion at the Collector Base if you hadn't been leading us."

"Thanks Jacob," Garrus replied, "but I'm sure we'd have done just as well with you in charge, better maybe. Can I get you a drink?"

"Sure, sounds good," said Jacob as he sat down at the small bar next to Garrus.

"You guys sure have been tearing through all the human beers," Garrus joked. "We're almost out."

"Yeah, I guess you're well-stocked though," Jacob said. "With Tali gone, you've got the dextros all to yourself. Then again, I can't imagine her drinking too much anyway."

Garrus laughed and said, "Don't let her bubbly little girl act fool you. Tali has more responsibility to deal with than any of us did at her age. Sure we've both commanded troops before but we were only responsible for a small squad at most and there were always plenty of people higher up the chain of command. Now she's at the top of it. She's an Admiral responsible for her entire race."

"Can't imagine that..." said Jacob.

"She wasn't even considered a full adult when she joined Shepard to help stop Saren," Garrus said. "Then she joined up with us again to fight the Collectors. She's seen more action than most ever do and she's got some great stories, especially after a few beers have made her more talkative."

"You two must be pretty close, after everything you've been through together," said Jacob.

"Yeah," Garrus replied. "She's a good friend..."

The lounge door opened and Miranda walked in. "Having a little guys' night and drinking on the job? I'm disappointed," she said. "

"Wha-?" Garrus started.

"-Disappointed that you didn't include Joker," Miranda continued. "I think he gets lonely up on the bridge, especially with the ship so empty as it is."

"You care about all of us now?" Garrus joked.

"I've always cared about this crew's safety and well-being," Miranda responded, "Couldn't survive a successful Collector Base assault without a full squad focused on the task. But we've been through a lot together and it's more than that now. You know that up until recently I had no family to speak of and well...I think all of us make a sort of _family _together. A good one."

"Likewise Miranda," Garrus replied happily, "I never pictured this happening back when we first met, but I'm glad you're here… And I'm sorry about all the crap I gave you and Shepard before. You guys are good for each other. And I may not trust Cerberus, but I trust _you_."

* * *

Cronos Station

Location Unknown

* * *

The Illusive Man lit a cigarette as he read over the various reports coming in from his intelligence network. He had known this day was coming for the past thirty years, ever since he was exposed to the Reaper Monolith on Shanxi, and he had been planning for it ever since. Cerberus had come a long way in the past year, thanks in large part to his scientists' study of the preserved Collector Base. Now it was time to put his plans and that technology into action.

"Are the prototypes ready, Agent Leng?" He asked.

"The first ten squadrons are combat ready, sir," Kai Leng answered. "They should be able to hold their own against a Reaper. The men are calling them, _Nephilim _class."

"Fitting name, given their origins," the Illusive Man said. "Their effectiveness will be tested soon enough. Which means it's time for _Commander Shepard_ to leave that prison cell back on Earth."

"With all due respect, sir, Shepard has already played his part," Leng replied. "Now he's a liability."

"Commander Shepard's _real _part in this was done as soon as Agent Lawson's team succeeded in _resurrecting_ him," the Illusive Man told him. "But he is still a very useful _asset _to us."

"His true loyalty is still to the Alliance," Leng said. "We're lucky he didn't betray us and turn that Base over to _them_ instead of Cerberus."

"That was not an unforeseen possibility," the Illusive Man said. "And it would not have affected our plans. The real value of the Collector Base was the _information_ it contained. Now that we know _how_ to reverse engineer their technology, we can manufacture it anywhere given the proper resources. Having the Base just makes it easier."

"And if the Alliance did get a hold of it?" Leng asked.

"They wouldn't know what to do with it," the Illusive Man replied. "They couldn't unlock its _full _potential. They don't have the _key_."

"The Cipher," Leng said.

"Exactly," the Illusive Man continued. "That was the Lazarus Project's _true_ goal. Commander Shepard's knowledge of the Reapers, status as a heroic symbol, and his many connections are all extremely beneficial to our cause. But those are all replacable. The _Prothean Cipher_ in his head is why we needed him alive."

"I'm surprised he hasn't caught on yet," Leng replied. "You spent billions of credits to bring him back, and then asked him to take on a _suicide mission_."

"Shepard may have his suspicions, but he's more focused on the Reapers at this point," the Illusive Man said. "As we _all _should be."

"Why wasn't Miranda told the true purpose of the Project?" Leng asked. "She _was_ in charge of it."

"Both her and Shepard had a mission to complete _after_ it was done," the Illusive Man said. "Knowing they were expendable would have greatly hindered their effectiveness. We had to let them _think_ that they were special, that their team was our _only _hope. Otherwise they wouldn't have done it."

* * *

Normandy Crew Deck Lounge

* * *

"I'm just curious, Miranda. Why the name _Cerberus_?" Garrus asked. "What does it mean?"

Before she could answer, EDI chimed in_: "Cerberus. A mythological three-headed canine, pet of Hades, the god of the dead, and guardian of the underworld in human Greek mythology."_

"I know _that_," Garrus said. "But what does it have to do with _human supremacy_? Why make their symbol a _dog_?"

"There's more to it," Miranda replied. "According to myth Hades was the god of the _earth_ itself, not just the underworld and the dead. Cerberus guarded its depths from those above."

"Ah, so you _guard_ the Earth and humanity from the other races," Garrus replied.

"Given that the _Charon_ Relay is Earth's gateway to the rest of the galaxy, the name seemed appropriate at the time, I suppose," Miranda told him. "A little ironic considering that for everyone else _we're_ the invasive newcomers."

"Do you guys think that everyone will just put these things aside and _work together_ when it's time to fight the Reapers?" Jacob asked.

"Humanity will," Garrus answered. "Compared to the rest of us, humans have a short memory. They'll welcome people who were once their enemies as allies pretty readily if the circumstances are right. The rest of us, I'm not so sure. Our bad blood goes _deeper_."

"If we're going to have _any_ chance at all in this war, they're going to have to," Jacob said.

"That's why we need _Shepard_," Garrus told him. "He's the one who can bring them all together."

* * *

Arcturus Station

February 27, 2186

* * *

"Sir, we're getting some _strange reports_ from the deep-field scanning team you put together," Colonel Harris said. "It was supposed to be _science _project, but now they're seeing some kind of _massive objects_ moving towards us at the _exact _coordinates you ordered them to look at. They're throwing off all kinds of energy signatures: heat, EM, dark energy…What is going on?"

"Get me Admiral Anderson on the line," Admiral Hackett said. "And send a message to command using the emergency codes. Tell them to start mobilizing everything we've got _right now._ The reports said the objects are moving towards us, how long until they get here?"

"About a week, give or take," the colonel replied.

* * *

Council Meeting Room

The Citadel

March 1, 2186

* * *

"Admiral Anderson, the Alliance military's actions over the past few days has been highly troubling," the Asari Councilor said to the QED-generated hologram in the middle of the room.

"Why has the Alliance military began a massive mobilization without the consent of its governing bodies and in direct violation of Council law?" Councilor Udina asked.

"This show of force has escalated border tensions all across the galaxy," the Turian Councilor said. "The other races are beginning a counter-mobilization effort in response to this _human aggression_. These rogue actions within your military have put us on the brink of war."

"They _should_ be mobilizing, Councilors," Anderson replied. "We _are_ on the brink of the war."

"Explain yourself," the Salarian Councilor said.

"We couldn't risk sending this information over an unsecured channel," Anderson said, as he pressed a few buttons on his Omni-tool and transferred some data files to the Council. "We're picking up something _massive_ on long range scanners, energy readings are consistent with _ships_ of some kind. It's not just space debris. They're headed this way, fast…We think it's the Reapers."

"Impossible…" the Turian Councilor said.

"The data is right in front of you," Anderson told him. "Reapers or not, _something_ is on its way here right now. We have less than a week until it reaches us."

"What would you have us do?" the Asari Councilor asked.

"Prepare for the worst," Anderson replied.

* * *

Alliance Command Center

Earth

March 2, 2186

* * *

Lieutenant James Vega entered Shepard's cell and saluted. "Commander," he said.

"You're not supposed to call me that anymore James," Shepard replied.

"Not supposed to salute you either," James said. "C'mon, we've got to go. The defense committee wants to see you."

"The committee?" Shepard asked as he followed James out of the room. "What's this about?"

"Couldn't say," James replied. "They just said they needed you…now."

Shepard saw Admiral Anderson approaching through a crowd of Alliance officials frantically checking their omni-tools and running off in different directions. This was serious.

"What's going on?" he asked the admiral. "Why is everyone in such a hurry?"

"Admiral Hackett's mobilizing the fleets," Anderson replied. "Something _big_ is headed our way."

"The Reapers?" Shepard asked.

"We don't know yet, not for certain," Anderson replied.

"What else _could_ it be?" Shepard said.

"If I knew that…" Anderson started.

"It's the Reapers," Shepard said grimly. "And we're not ready for them. Not by a long shot."

"Tell that to the defense committee," Anderson said.

"It's too late for that," Shepard replied. "They should have listened when I warned them _two years ago_."

"I agree with you, but this isn't the time Shepard," Anderson told him. "Right now we need to focus on stopping the Reapers, and you know more about this enemy than anyone. Do you want to waste what little time we have left complaining about how the Alliance handled this or do you want to help us _do _something about it?"

Shepard and Anderson entered the war room and approached the central table the committee was gathered around.

"Has Shepard been briefed?" Admiral Mikhailovich asked.

"Well enough," Anderson replied.

"Good," Mikhailovich said. "Let's get straight to the point then. You're the expert on these things, Shepard. The Alliance as a whole may not have believed you before, and I'm sorry for that, but you've got our attention now. _What do we do_?"

"I'm a soldier, not a strategist," Shepard responded. "I command small strike teams, not entire fleet. That being said, based on what I know about their past incursions from the Prothean A.I. on Ilos I do have some ideas about how to fight the Reapers… but you're not going to like them."

"We'll do what we have to," Mikhailovich replied. "Whatever it takes. Go on."

"The best way to fight these things is to stay mobile," Shepard continued. "They'll hit our supply lines fast, so whatever resources you've got: food, weapons, ammo, unload all of it _now_, before we lose it. The Reapers do things systematically, world by world, system by system. We don't stand a chance against them in a stand up fight and static defenses are practically useless against them. Arcturus Station, the colonies, even _Earth_ will fall easily. Don't waste our ships defending them. It's a lost cause."

"Just abandon the people we're sworn to protect?" Anderson asked.

"We have no choice," Shepard answered. "Even if we did try to defend them, the Reapers would cut through our lines like butter. Our best option is to retreat initially, then hit the Reapers with a series of counter-attacks from their flanks. Harass them with guerilla warfare as a delaying tactic."

"Delaying tactic for what?" Anderson asked.

"To give the rest of the galaxy more time to prepare," Shepard replied. "…And for Cerberus to try and complete their _secret weapon_."

The room went silent. After a moment Admiral Anderson said, "You said you told us everything, Shepard."

"I lied," Commander Shepard replied.

* * *

Alliance News Network Broadcast

March 4, 2186

* * *

_FLOOD OF BATARIAN TRAFFIC BRINGS RUMORS OF WAR_

_UTOPIA SYSTEM – A massive influx of Batarian ships is raising tensions in the Exodus Cluster, putting Alliance forces on high alert. According to Alliance officials, the ships came from the Batarian-held Harsa relay with minimal warning, some barreling right through. The Alliance reportedly fired on some of the ships with the intent to disable them._

"It's a miracle any of them are still alive_," one human frigate captain said. According to the Batarians, they are neither invaders nor defectors, but refugees. They claim a hostile species has attacked the Hegemony's fleet, bombarding Khar'shan and other batarian planets._

_With the Harsa comm buoy system crippled, communication is sporadic at best between far-flung Batarians and their government on Khar'shan. Some refugees claim the attackers were Council. Others blame the Geth or even the Rachni. All report that the enemy, in whatever form, is blockading the relay, destroying most spacecraft trying to make it through. The refugees are not solely civilians. Hegemony Commander, Eruz Mathat, who is under guard while his cruiser is inspected, was blunt in his assessment of the situation. "_I never thought I would say this to the human navy_," he said, "_but we need you_."_

* * *

Normandy Bridge

* * *

"Oh no," Kasumi said worriedly. "No, no, no, no… they're really here."

"That _has_ to be them on Khar'Shan," Jacob said. "Still…I thought we'd have more time."

"We _did_ have more time," Miranda told him as she paced the bridge. "Between stopping _Sovereign _at the Citadel and destroying the Alpha Relay Shepard bought us _three years_. If the Alliance hadn't come after him…or if he hadn't turned himself over to them…maybe he could have found another way to stall them, stop them even…I don't know, dammit."

"He did everything he could," Garrus replied, overlooking the galaxy map. "He cut off all their shortcuts, but we couldn't stop them from just flying here on their own. And taking the long way must have cost them a _ton_ of energy. He helped wear them down a little at least."

"I hope you're right," Miranda said. "But as powerful as they are, does it even matter if they're not at full strength? The combined dreadnoughts of several fleets were barely enough to beat _Sovereign_, and that was _after_ Shepard took down its shields."

"It doesn't matter now," Garrus said. "We've got some better tech on our ships now. Maybe that will be enough to stop them, maybe not, but either way we have to face them now."

"We're going to need Shepard for that," Miranda said. "EDI, set a course for Earth… and contact the Illusive Man. If Cerberus really does have a plan for fighting these things, now's the time."

* * *

Alliance Command Center

Earth

March 5, 2186

* * *

"Why did you lie to us, Shepard?" Anderson asked. "To _me_?"

"It doesn't matter now," Shepard replied.

"The _hell_ it doesn't!" Anderson told him. "I thought we were in this together. I've risked my career for you _more_ than once, because I _trusted _you. And you've been lying to us this _whole_ time."

"I didn't have a choice," Shepard said. "If I _had_ told the Alliance about Cerberus's plans they would have tried to stop them, started a war with Cerberus. _Both_ sides can't afford that, just like we couldn't afford to start a war with the Batarians. That _weapon_ they're working on could be our _best_ chance against the Reapers."

"And you _trust_ them with it?" Anderson asked. "You've seen their sick experiments, how reckless they are with dangerous technology. You really think they'll _only_ use it against the Reapers?"

"They were the only ones set up to do this," Shepard replied. "Transfer to the Alliance would have taken too long, and we had to do _something_ with that technology. You know our military doesn't stand a chance against the Reapers as it is."

"So you gambled on Cerberus instead?" Anderson asked. "That's a hell of a risk."

"It was the _tactical_ choice," Shepard said. "Maybe it was a bad idea, maybe it wasn't, but if I had done nothing or destroyed that tech we'd _definitely _be doomed. A chance is better than nothing."

"You really think this will work?" Anderson asked him.

"I don't know," Shepard replied. "But it's our only shot at this point. What else _can _we do?"

"You're betting _everything_ on this," Anderson said. "Is it really worth it? Abandoning the people we're supposed to protect, just throwing them to the Reapers to buy time?"

"The Alliance _can't_ protect them," Shepard answered. "How long do you think they can hold out against an entire _fleet_ of Reapers? A few hours maybe, if that. Earth _will _fall… but we can take it back. I'll do my best to fight them here, protect who I can until the cavalry comes."

"Forget it," Anderson said. "You're leaving. I'll handle the frontlines. We need you to lead the counterattack. Rally our allies, everything we've got. That's an order."

"I don't take orders from you anymore," Shepard replied. "Remember?"

"Consider yourself reinstated, _Commander,_" Anderson said as he handed him his Alliance dog tags.


End file.
